OK, this is officially a mystery. AP's developer Ray Gralak replied with a video showing that there is no reversal in their software either.

https://www.dropbox.com/s/10ac4a0x6u...nRate.mp4?dl=0

Craig I need to call you and go back over the info here, and probably do some live testing. I am clearly missing something. How can I be setting the RightAscensionRate to a negative number and it's coming out positive in the AP driver?

When can we talk and do some tests on your observatory? It can be during the day as long as you either have a dome or safe roof, or can open the roof and cover the scope from the sun.